Our office scanner has been cunningly designed so as to have an automatic document feeder, but to only be capable of scanning the upward-facing side of each page! Here are two PDFtk commands to help deal with this.
pdftk in*pdf cat output out.pdf
Collation with the backs in reverse order, because when the stack is turned over to scan the backs, it scans the last page first:
pdftk A=fronts.pdf B=backs.pdf shuffle A Bend-1 output out.pdf